Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters

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Abstract
In this paper we present a new method for predicting a set of RNA secondary structures that are thermodynamlcally favored In RNA folding simulations. This method uses a large number of ‘simulated energy rules’ (SER) generated by perturbing the free energy parameters derived experimentally within the range of the experimental errors. The structure with the lowest free energy is computed for each SER. Structural comparisons are used to avoid multiple generation of similar structures. Computed structures are evaluated using the energy distribution of the lowest free energy structures derived In the simulation. Predicted structures and all possible occurring helical stems can be graphically displayed with their occurring frequencies in the simulation by dot-plot representations. On average, about 90% of phylogenetlc helixes in the known models of tRNA, Group I self-splicing Intron, and Escheiichla coll 16 S rRNA, were predicted using the method.